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PLoS Genetics

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https://www.readbyqxmd.com/read/30235212/modulation-of-acd6-dependent-hyperimmunity-by-natural-alleles-of-an-arabidopsis-thaliana-nlr-resistance-gene
#1
Wangsheng Zhu, Maricris Zaidem, Anna-Lena Van de Weyer, Rafal M Gutaker, Eunyoung Chae, Sang-Tae Kim, Felix Bemm, Lei Li, Marco Todesco, Rebecca Schwab, Frederik Unger, Marcel Janis Beha, Monika Demar, Detlef Weigel
Plants defend themselves against pathogens by activating an array of immune responses. Unfortunately, immunity programs may also cause unintended collateral damage to the plant itself. The quantitative disease resistance gene ACCELERATED CELL DEATH 6 (ACD6) serves to balance growth and pathogen resistance in natural populations of Arabidopsis thaliana. An autoimmune allele, ACD6-Est, which strongly reduces growth under specific laboratory conditions, is found in over 10% of wild strains. There is, however, extensive variation in the strength of the autoimmune phenotype expressed by strains with an ACD6-Est allele, indicative of genetic modifiers...
September 20, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/30231021/balancing-selection-on-a-recessive-lethal-deletion-with-pleiotropic-effects-on-two-neighboring-genes-in-the-porcine-genome
#2
Martijn F L Derks, Marcos S Lopes, Mirte Bosse, Ole Madsen, Bert Dibbits, Barbara Harlizius, Martien A M Groenen, Hendrik-Jan Megens
Livestock populations can be used to study recessive defects caused by deleterious alleles. The frequency of deleterious alleles including recessive lethal alleles can stay at high or moderate frequency within a population, especially if recessive lethal alleles exhibit an advantage for favourable traits in heterozygotes. In this study, we report such a recessive lethal deletion of 212kb (del) within the BBS9 gene in a breeding population of pigs. The deletion produces a truncated BBS9 protein expected to cause a complete loss-of-function, and we find a reduction of approximately 20% on the total number of piglets born from carrier by carrier matings...
September 19, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/30226839/evolution-of-endothelin-signaling-and-diversification-of-adult-pigment-pattern-in-danio-fishes
#3
Jessica E Spiewak, Emily J Bain, Jin Liu, Kellie Kou, Samantha L Sturiale, Larissa B Patterson, Parham Diba, Judith S Eisen, Ingo Braasch, Julia Ganz, David M Parichy
Fishes of the genus Danio exhibit diverse pigment patterns that serve as useful models for understanding the genes and cell behaviors underlying the evolution of adult form. Among these species, zebrafish D. rerio exhibit several dark stripes of melanophores with sparse iridophores that alternate with light interstripes of dense iridophores and xanthophores. By contrast, the closely related species D. nigrofasciatus has an attenuated pattern with fewer melanophores, stripes and interstripes. Here we demonstrate species differences in iridophore development that presage the fully formed patterns...
September 18, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/30226838/detecting-archaic-introgression-using-an-unadmixed-outgroup
#4
Laurits Skov, Ruoyun Hui, Vladimir Shchur, Asger Hobolth, Aylwyn Scally, Mikkel Heide Schierup, Richard Durbin
Human populations outside of Africa have experienced at least two bouts of introgression from archaic humans, from Neanderthals and Denisovans. In Papuans there is prior evidence of both these introgressions. Here we present a new approach to detect segments of individual genomes of archaic origin without using an archaic reference genome. The approach is based on a hidden Markov model that identifies genomic regions with a high density of single nucleotide variants (SNVs) not seen in unadmixed populations...
September 18, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/30222786/mapk-and-gsk3-%C3%A3-trcp-mediated-degradation-of-the-maternal-ets-domain-transcriptional-repressor-yan-tel-controls-the-spatial-expression-of-nodal-in-the-sea-urchin-embryo
#5
M Dolores Molina, Magali Quirin, Emmanuel Haillot, Noémie De Crozé, Ryan Range, Mathieu Rouel, Felipe Jimenez, Radja Amrouche, Aline Chessel, Thierry Lepage
In the sea urchin embryo, specification of the dorsal-ventral axis critically relies on the spatially restricted expression of nodal in the presumptive ventral ectoderm. The ventral restriction of nodal expression requires the activity of the maternal TGF-beta ligand Panda but the mechanism by which Panda restricts nodal expression is unknown. Similarly, what initiates expression of nodal in the ectoderm and what are the mechanisms that link patterning along the primary and secondary axes is not well understood...
September 17, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/30222779/disrupted-structure-and-aberrant-function-of-chip-mediates-the-loss-of-motor-and-cognitive-function-in-preclinical-models-of-scar16
#6
Chang-He Shi, Carrie Rubel, Sarah E Soss, Rebekah Sanchez-Hodge, Shuo Zhang, Sabrina C Madrigal, Saranya Ravi, Holly McDonough, Richard C Page, Walter J Chazin, Cam Patterson, Cheng-Yuan Mao, Monte S Willis, Hai-Yang Luo, Yu-Sheng Li, Donte A Stevens, Mi-Bo Tang, Pan Du, Yao-He Wang, Zheng-Wei Hu, Yu-Ming Xu, Jonathan C Schisler
CHIP (carboxyl terminus of heat shock 70-interacting protein) has long been recognized as an active member of the cellular protein quality control system given the ability of CHIP to function as both a co-chaperone and ubiquitin ligase. We discovered a genetic disease, now known as spinocerebellar autosomal recessive 16 (SCAR16), resulting from a coding mutation that caused a loss of CHIP ubiquitin ligase function. The initial mutation describing SCAR16 was a missense mutation in the ubiquitin ligase domain of CHIP (p...
September 17, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/30222737/topoisomerases-i-and-iii-inhibit-r-loop-formation-to-prevent-unregulated-replication-in-the-chromosomal-ter-region-of-escherichia-coli
#7
Julien Brochu, Émilie Vlachos-Breton, Sarah Sutherland, Makisha Martel, Marc Drolet
Type 1A topoisomerases (topos) are the only ubiquitous topos. E. coli has two type 1A topos, topo I (topA) and topo III (topB). Topo I relaxes negative supercoiling in part to inhibit R-loop formation. To grow, topA mutants acquire compensatory mutations, base substitutions in gyrA or gyrB (gyrase) or amplifications of a DNA region including parC and parE (topo IV). topB mutants grow normally and topo III binds tightly to single-stranded DNA. What functions topo I and III share in vivo and how cells lacking these important enzymes can survive is unclear...
September 17, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/30222730/the-topoisomerase-3%C3%AE-zinc-finger-domain-t1-of-arabidopsis-thaliana-is-required-for-targeting-the-enzyme-activity-to-holliday-junction-like-dna-repair-intermediates
#8
Annika Dorn, Sarah Röhrig, Kristin Papp, Susan Schröpfer, Frank Hartung, Alexander Knoll, Holger Puchta
Topoisomerase 3α, a class I topoisomerase, consists of a TOPRIM domain, an active centre and a variable number of zinc-finger domains (ZFDs) at the C-terminus, in multicellular organisms. Whereas the functions of the TOPRIM domain and the active centre are known, the specific role of the ZFDs is still obscure. In contrast to mammals where a knockout of TOP3α leads to lethality, we found that CRISPR/Cas induced mutants in Arabidopsis are viable but show growth retardation and meiotic defects, which can be reversed by the expression of the complete protein...
September 17, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/30216339/activating-pax-gene-family-paralogs-to-complement-pax5-leukemia-driver-mutations
#9
Matthew R Hart, Donovan J Anderson, Christopher C Porter, Tobias Neff, Michael Levin, Marshall S Horwitz
PAX5, one of nine members of the mammalian paired box (PAX) family of transcription factors, plays an important role in B cell development. Approximately one-third of individuals with pre-B acute lymphoblastic leukemia (ALL) acquire heterozygous inactivating mutations of PAX5 in malignant cells, and heterozygous germline loss-of-function PAX5 mutations cause autosomal dominant predisposition to ALL. At least in mice, Pax5 is required for pre-B cell maturation, and leukemic remission occurs when Pax5 expression is restored in a Pax5-deficient mouse model of ALL...
September 14, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/30212491/pan-cancer-inference-of-intra-tumor-heterogeneity-reveals-associations-with-different-forms-of-genomic-instability
#10
Franck Raynaud, Marco Mina, Daniele Tavernari, Giovanni Ciriello
Genomic instability is a major driver of intra-tumor heterogeneity. However, unstable genomes often exhibit different molecular and clinical phenotypes, which are associated with distinct mutational processes. Here, we algorithmically inferred the clonal phylogenies of 6,000 human tumors from 32 tumor types to explore how intra-tumor heterogeneity depends on different implementations of genomic instability. We found that extremely unstable tumors associated with DNA repair deficiencies or high chromosomal instability are not the most intrinsically heterogeneous...
September 13, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/30208061/robust-activation-of-microhomology-mediated-end-joining-for-precision-gene-editing-applications
#11
Hirotaka Ata, Thomas L Ekstrom, Gabriel Martínez-Gálvez, Carla M Mann, Alexey V Dvornikov, Kyle J Schaefbauer, Alvin C Ma, Drena Dobbs, Karl J Clark, Stephen C Ekker
One key problem in precision genome editing is the unpredictable plurality of sequence outcomes at the site of targeted DNA double stranded breaks (DSBs). This is due to the typical activation of the versatile Non-homologous End Joining (NHEJ) pathway. Such unpredictability limits the utility of somatic gene editing for applications including gene therapy and functional genomics. For germline editing work, the accurate reproduction of the identical alleles using NHEJ is a labor intensive process. In this study, we propose Microhomology-mediated End Joining (MMEJ) as a viable solution for improving somatic sequence homogeneity in vivo, capable of generating a single predictable allele at high rates (56% ~ 86% of the entire mutant allele pool)...
September 12, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/30208021/transcription-factor-cbf-1-is-critical-for-circadian-gene-expression-by-modulating-white-collar-complex-recruitment-to-the-frq-locus
#12
Xuemei Cao, Xiao Liu, Hongda Li, Yumeng Fan, Jiabin Duan, Yi Liu, Qun He
Transcription of the Neurospora crassa circadian clock gene frequency (frq) is an essential process in the negative feedback loop that controls circadian rhythms. WHITE COLLAR 1 (WC-1) and WHITE COLLAR 2 (WC-2) forms the WC complex (WCC) that is the main activator of frq transcription by binding to its promoter. Here, we show that Centromere Binding Factor 1 (CBF-1) is a critical component of the N. crassa circadian clock by regulating frq transcription. Deletion of cbf-1 resulted in long period and low amplitude rhythms, whereas overexpression of CBF-1 abolished the circadian rhythms...
September 12, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/30192747/nicotinamide-n-methyltransferase-controls-behavior-neurodegeneration-and-lifespan-by-regulating-neuronal-autophagy
#13
Kathrin Schmeisser, J Alex Parker
Nicotinamide N-methyl-transferase (NNMT) is an essential contributor to various metabolic and epigenetic processes, including the regulating of aging, cellular stress response, and body weight gain. Epidemiological studies show that NNMT is a risk factor for psychiatric diseases like schizophrenia and neurodegeneration, especially Parkinson's disease (PD), but its neuronal mechanisms of action remain obscure. Here, we describe the role of neuronal NNMT using C. elegans. We discovered that ANMT-1, the nematode NNMT ortholog, competes with the methyltransferase LCMT-1 for methyl groups from S-adenosyl methionine...
September 7, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/30212501/2018-plos-genetics-research-prize-bundling-stabilizing-organizing-the-orchestration-of-acentriolar-spindle-assembly-by-microtubule-motor-proteins
#14
EDITORIAL
Gregory S Barsh, Needhi Bhalla, Francesca Cole, Gregory P Copenhaver, Soni Lacefield, Diana E Libuda
No abstract text is available yet for this article.
September 2018: PLoS Genetics
https://www.readbyqxmd.com/read/30212495/correction-whole-exome-sequencing-reveals-hspa1l-as-a-genetic-risk-factor-for-spontaneous-preterm-birth
#15
Johanna M Huusko, Minna K Karjalainen, Britney E Graham, Ge Zhang, Emily G Farrow, Neil A Miller, Bo Jacobsson, Haley R Eidem, Jeffrey C Murray, Bruce Bedell, Patrick Breheny, Noah W Brown, Frans L Bødker, Nadia K Litterman, Pan-Pan Jiang, Laura Russell, David A Hinds, Youna Hu, Antonis Rokas, Kari Teramo, Kaare Christensen, Scott M Williams, Mika Rämet, Stephen F Kingsmore, Kelli K Ryckman, Mikko Hallman, Louis J Muglia
[This corrects the article DOI: 10.1371/journal.pgen.1007394.].
September 2018: PLoS Genetics
https://www.readbyqxmd.com/read/30212463/flexibility-and-constraint-evolutionary-remodeling-of-the-sporulation-initiation-pathway-in-firmicutes
#16
Philip Davidson, Rory Eutsey, Brendan Redler, N Luisa Hiller, Michael T Laub, Dannie Durand
The evolution of signal transduction pathways is constrained by the requirements of signal fidelity, yet flexibility is necessary to allow pathway remodeling in response to environmental challenges. A detailed understanding of how flexibility and constraint shape bacterial two component signaling systems is emerging, but how new signal transduction architectures arise remains unclear. Here, we investigate pathway remodeling using the Firmicute sporulation initiation (Spo0) pathway as a model. The present-day Spo0 pathways in Bacilli and Clostridia share common ancestry, but possess different architectures...
September 2018: PLoS Genetics
https://www.readbyqxmd.com/read/30212449/structure-and-function-of-archaeal-histones
#17
REVIEW
Bram Henneman, Clara van Emmerik, Hugo van Ingen, Remus T Dame
The genomes of all organisms throughout the tree of life are compacted and organized in chromatin by association of chromatin proteins. Eukaryotic genomes encode histones, which are assembled on the genome into octamers, yielding nucleosomes. Post-translational modifications of the histones, which occur mostly on their N-terminal tails, define the functional state of chromatin. Like eukaryotes, most archaeal genomes encode histones, which are believed to be involved in the compaction and organization of their genomes...
September 2018: PLoS Genetics
https://www.readbyqxmd.com/read/30199545/physiological-and-pathological-roles-of-fatp-mediated-lipid-droplets-in-drosophila-and-mice-retina
#18
Daan M Van Den Brink, Aurélie Cubizolle, Gilles Chatelain, Nathalie Davoust, Victor Girard, Simone Johansen, Francesco Napoletano, Pierre Dourlen, Laurent Guillou, Claire Angebault-Prouteau, Nathalie Bernoud-Hubac, Michel Guichardant, Philippe Brabet, Bertrand Mollereau
Increasing evidence suggests that dysregulation of lipid metabolism is associated with neurodegeneration in retinal diseases such as age-related macular degeneration and in brain disorders such as Alzheimer's and Parkinson's diseases. Lipid storage organelles (lipid droplets, LDs), accumulate in many cell types in response to stress, and it is now clear that LDs function not only as lipid stores but also as dynamic regulators of the stress response. However, whether these LDs are always protective or can also be deleterious to the cell is unknown...
September 2018: PLoS Genetics
https://www.readbyqxmd.com/read/30199539/reduced-monocyte-and-macrophage-tnfsf15-tl1a-expression-is-associated-with-susceptibility-to-inflammatory-bowel-disease
#19
Arianne C Richard, James E Peters, Natalia Savinykh, James C Lee, Eric T Hawley, Françoise Meylan, Richard M Siegel, Paul A Lyons, Kenneth G C Smith
Chronic inflammation in inflammatory bowel disease (IBD) results from a breakdown of intestinal immune homeostasis and compromise of the intestinal barrier. Genome-wide association studies have identified over 200 genetic loci associated with risk for IBD, but the functional mechanisms of most of these genetic variants remain unknown. Polymorphisms at the TNFSF15 locus, which encodes the TNF superfamily cytokine commonly known as TL1A, are associated with susceptibility to IBD in multiple ethnic groups. In a wide variety of murine models of inflammation including models of IBD, TNFSF15 promotes immunopathology by signaling through its receptor DR3...
September 2018: PLoS Genetics
https://www.readbyqxmd.com/read/30199527/mir-202-controls-female-fecundity-by-regulating-medaka-oogenesis
#20
Stéphanie Gay, Jérôme Bugeon, Amine Bouchareb, Laure Henry, Clara Delahaye, Fabrice Legeai, Jérôme Montfort, Aurélie Le Cam, Anne Siegel, Julien Bobe, Violette Thermes
Female gamete production relies on coordinated molecular and cellular processes that occur in the ovary throughout oogenesis. In fish, as in other vertebrates, these processes have been extensively studied both in terms of endocrine/paracrine regulation and protein expression and activity. The role of small non-coding RNAs in the regulation of animal reproduction remains however largely unknown and poorly investigated, despite a growing interest for the importance of miRNAs in a wide variety of biological processes...
September 2018: PLoS Genetics
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